Biology subjects

Nawaz, A.

Publications and source records attributed to Nawaz, A..

5 recordsLinked to original sources

bioRxiv2024

Isolation and Identification of P(3HB)-Degrading Bacteria from Malaysian Environment

The aim of this study was to identify Poly(3-hydroxybutyrate) [P(3HB)] degrading bacterial strains in Penang Malaysia. Samples were collected from various locations in Penang. Five isolates (SMA-1, SMB-2, SMC-3, SMD-4, and SME-5) with highest P(3HB) degradation indices were isolated through meticulous screening. These gram-negative bacilli were characterized first morphologically and then through scanning electron microscopy. Growth profiles of the isolates revealed that at 24 hrs, SME-5 showed the highest growth rate. Maximum depolymerase enzyme activity for all five isolates was observed after 72 hrs. 16S rDNA sequencing identified all isolates as Comamonas testosteroni. This study provides insights into the growth characteristics and extracellular depolymerase activity of P(3HB)-degrading bacteria isolated from the Malaysian environment. It highlights the potential of Comamonas testosteroni strains as P(3HB) bioplastic degraders in diverse habitats.

microbiology↗

bioRxiv2024

Exploring environmental microfungal diversity through serial single cell screening

Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology, and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realized by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify thirty-two potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterize the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.

microbiology↗

bioRxiv2024

Augmentation of DNA exonuclease TREX1 in macrophages as a therapy for cardiac ischemic injury

Noncoding RNAs (ncRNAs) are increasingly recognized as bioactive. Here we report the development of TY1, a synthetic ncRNA bioinspired by a naturally-occurring human small Y RNA with immunomodulatory properties. TY1 upregulates TREX1, an exonuclease that rapidly degrades cytosolic DNA. In preclinical models of myocardial infarction (MI) induced by ischemia/reperfusion, TY1 reduced scar size. The cardioprotective effect of TY1 was abrogated by prior depletion of macrophages and mimicked by adoptive transfer of macrophages exposed either to TY1 or TREX1. Inhibition of TREX1 in macrophages blocked TY1 cardioprotection. Consistent with a central role for TREX1, TY1 attenuated DNA damage in the post-MI heart. This novel mechanism--pharmacologic upregulation of TREX1 in macrophages--establishes TY1 as the prototype for a new class of ncRNA drugs with disease-modifying bioactivity. One Sentence SummaryUpregulation of three prime exonuclease, TREX1, in macrophages enhances tissue repair post myocardial infarction.

molecular biology↗

bioRxiv2023

Exploring the Therapeutic Potential of Cannabis Constituents in Parkinson's Disease: Insights from Molecular Docking Studies

Cannabis, often known as marihuana, marijuana, hashish, and hash, belongs to the genus Cannabis sativa L. This plant has excellent potential for the treatment of several brain disorders. Phytochemical compounds in this plant act as antioxidants, preserving synaptic plasticity and preventing neuronal degeneration. The neurodegenerative condition Parkinsons has emerged as one of the most significant health concerns of the twenty-first century. A detailed in silico molecular docking study was carried out to assess the neuroprotective effects of cannabis compounds against four potential targets of PD, including monoamine oxidase B (MAO-B), catechol-O-methyltransferase (COMT), alpha-synuclein (ASN), and Adenosine A2A receptor (A2A). Physicochemical properties, drug-likeness, toxicity, and ADMET profiles were also investigated. In this docking study, the cannabis compound cannabicyclol showed a superior docking score of -10.8 kcal/mol with the MAO-B protein. Based on these results, cannabicyclol and the target protein MAO-B were used to perform MD simulations to analyze their stability at 100 ns. Furthermore, it is crucial to carry out in vitro and in vivo investigations to enhance the potency of cannabis components and understand the processes underlying the suppression of Parkinsons disease-related enzymes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/566677v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@15f455borg.highwire.dtl.DTLVardef@1c26038org.highwire.dtl.DTLVardef@3b32c6org.highwire.dtl.DTLVardef@82926b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Isoxanthohumol improves obesity and glucose metabolism via inhibiting intestinal lipid absorption with a bloom of Akkermansia muciniphila in mice

AimsDysbiosis is an important factor that leads to metabolic disorders by disrupting energy balance and insulin sensitivity. A decrease in Akkermansia muciniphila is a phenotype of obesity-induced dysbiosis. Although interventions to increase A. muciniphila are expected to improve glucose metabolism, the underlying mechanism has not been fully understood. MethodsIsoxanthohumol (IX), a prenylated flavonoid found in beer hops was administered to high fat diet-fed mice. We analyzed glucose metabolism, gene expression profiles and histology of liver, epididymal adipose tissue and colon. Lipase activity, fecal lipid profiles and plasma metabolomic analysis were assessed. Fecal 16s rRNA sequencing was obtained and selected bacterial species were used for in vitro studies. Fecal microbiota transplantation and monocolonization were conducted to antibiotic-treated or germ-free (GF) mice. ResultsThe administration of IX lowered weight gain, decreased steatohepatitis and improved glucose metabolism. Mechanistically, IX inhibited pancreatic lipase activity and lipid absorption by decreasing the expression of the fatty acid transporter CD36 in the small intestine, which was confirmed by increased lipid excretion in feces. IX administration improved the gut barrier function and reduced metabolic endotoxemia. In contrast, the effects of IX were nullified by antibiotics. As revealed using 16S rRNA sequencing, the microbial community structure changed with a significant increase in the abundance of A. muciniphila in the IX-treated group. An anaerobic chamber study showed that IX selectively promoted the growth of A. muciniphila while exhibiting antimicrobial activity against some Bacteroides and Clostridium species. To further explore the direct effect of A. muciniphila on lipid and glucose metabolism, we monocolonized either A. muciniphila or Bacteroides thetaiotaomicron to GF mice. A. muciniphila monocolonization decreased CD36 expression in the jejunum and improved glucose metabolism, with decreased levels of multiple classes of fatty acids determined using plasma metabolomic analysis. ConclusionOur study confirmed a direct role of A. muciniphila in energy metabolism, which was induced by microbial actions of IX. These highlight new treatment strategies for preventing metabolic syndrome by boosting the gut microbiota with food components.

microbiology↗